AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_bbur_reg_300.orf -o00252_bbur_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 BB0101 156 asparaginyl-tRNA synthetase (asnS) #2 BB0155 61 B. burgdorferi predicted coding region BB0155 #3 BB0156 28 B. burgdorferi predicted coding region BB0156 #4 BB0158 153 antigen, S2, putative #5 BB0159 23 B. burgdorferi predicted coding region BB0159 #6 BB0160 47 alanine racemase (alr) #7 BB0224 68 B. burgdorferi predicted coding region BB0224 #8 BB0446 243 aspartyl-tRNA synthetase (aspS) #9 BB0452 90 B. burgdorferi predicted coding region BB0452 #10 BB0605 70 serine-type D-Ala-D-Ala carboxypeptidase (dacA) #11 BB0608 116 aminoacyl-histidine dipeptidase (pepD) Motif number 1 TTGTTAATATTTATACTTTACTTTTTAGGGGTGATTA 1 21 0 TTATTTTTTA 0.975527 -136 TTAACAATTTTTATTATTTTAATTCTTGATATTAACT 1 58 0 TTATTTATTT 0.925524 -99 TTATTATAGCTTAAAACTTTTTTTAAAAAAAACATTT 1 93 0 TTACTTTTTA 0.843194 -64 CTTATTAATATTGTTAAATCAATTTTATTATAGCTTA 1 117 0 TTGAATATTA 0.768675 -40 ATTTTTATATTATTATTTAAAATGACTTTAA 2 41 0 TTATATTTTA 0.88897 -21 TTATTTAAAATTGCATTTTTATTTTTAATCTTTCAAT 4 14 0 TTGTTTTTTA 0.948072 -140 GTCAAGTCGCTTTTGGTTTTATTTAAAATTGCATTTT 4 32 0 TTTTTTTTTA 0.949277 -122 TAGGCGGTAATTAAAATTTACATTAAATCATAGTAAT 4 91 0 TTATTTATTA 0.969173 -63 AAGATATTTCCTTTTGTTTTTAT 5 1 0 TTTTTTTTTT 0.840474 -23 TAAAAATCTTTTTTCTATTAATTTGTAGT 6 3 0 TTTATTTTTA 0.937829 -45 GATTTAACAATTATTTATTCTTTTTTAGGAGGAATTG 7 38 1 TTAATTTTTA 0.969815 -31 TGTCTATCAATTTTTCATTCAATTCATTACATTTGAT 8 26 0 TTTATTATTT 0.824643 -218 AAAATAAAACTTGAATATTGCATTAAAATTCAAGGAC 8 194 1 TTGATTATTA 0.942263 -50 TGTTTTAATTAGGGTTTTTATTGGAAGGCTTGTTT 9 66 0 TTATTTATTA 0.977848 -25 AAATGGCTCCTTTTTAATTGTATTGTAATTAACAATC 10 13 1 TTTATTATTA 0.943518 -58 AAATTATATATTATTTATTGATTGTTAATTACAATAC 10 32 0 TTAATTTTGA 0.773087 -39 ATATACTAAATTAATCTTTAAATTCATTCAATAAATT 11 23 0 TTATTTATTT 0.925521 -94 ATTTAGTATATTATATTATTAATTATAAATTAAATCC 11 49 1 TTATATATTA 0.899568 -68 CCAAGTATATTTATGGATTTAATTTAATCAAAGGAAA 11 84 1 TTAATTATTA 0.972662 -33 *** *** *** * Masking position 9 Map Score: 26.031 Number of sites scoring better than the average of aligned sites = 2264 Number in coding regions = 1433 Number in noncoding regions = 831 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 TACAAAATAATAATCACCCCTAAAAA 1 6 1 AATAATAATA 0.923668 -151 CTAAAAAGTAAAGTATAAATATTAACAAAGT 1 30 1 AAGTATAAAA 0.877459 -127 CAAGAATTAAAATAATAAAAATTGTTAAATG 1 67 1 AATAATAAAA 0.956584 -90 TTGTTAAATCAATTTTATTATAGCTTAAAAC 1 113 0 AATTTTATTT 0.608743 -44 TTGATTTAACAATATTAATAAGTTAAGTATT 1 132 1 AATATTAATA 0.923668 -25 CATTTTAAATAATAATATAAAAAT 2 48 1 AATAATATAA 0.937002 -14 GATATTGAAAGATTAAAAATAAAAATGCA 4 9 1 AAGATTAAAA 0.928764 -145 ATAAAAATGCAATTTTAAATAAAACCAAAAG 4 29 1 AATTTTAAAA 0.922721 -125 AAATCATAGTAATAATATAGAATGCTAATGT 4 73 0 AATAATATAA 0.937002 -81 ATTTAATGTAAATTTTAATTACCGCCTAAAA 4 100 1 AATTTTAATA 0.869191 -54 TTTATTCTAACATATTATATA 7 1 0 CATATTATAA 0.599236 -68 CCTCCTAAAAAAGAATAAATAATTGTTAAAT 7 39 0 AAGAATAAAA 0.928764 -30 TACATTTGATAACTTTAAACATAAC 8 5 0 AACTTTAAAA 0.621474 -239 ACAATCAATAAATAATATATAATTTTAATAT 10 44 1 AATAATATAA 0.936984 -27 GTTGTAATATTAAAATTATATATTAT 10 55 0 AATATTAAAT 0.8837 -16 CCAATATTATTGAATTTATTGAA 11 3 1 AATATTATTA 0.890933 -114 AATGAATTTAAAGATTAATTTAGTATATTAT 11 32 1 AAGATTAATT 0.712918 -85 ATTTATAATTAATAATATAATATACTAAATT 11 48 0 AATAATATAT 0.837611 -69 TTATATTATTAATTATAAATTAAATCCAAGT 11 59 1 AATTATAAAT 0.806791 -58 AATTAAATCCAAGTATATTTATGGATTTAAT 11 76 1 AAGTATATTA 0.726387 -41 ********* * Masking position 6 Map Score: 25.1081 Number of sites scoring better than the average of aligned sites = 1969 Number in coding regions = 1204 Number in noncoding regions = 765 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 3 AAGTTTTAAGCTATAATAAAATTGATTTAACAA 1 111 1 CTTATAAATT 0.912243 -46 TTTAAAATGACTTTAAGTCAATTATTTAGGAGA 2 24 0 CTTAGTAATT 0.949209 -38 TATATTATTACTATGATTTAATGTAAATTTTAA 4 85 1 CTTATTAATG 0.931963 -69 GTCTATCAATTTTTCATTCAATTCATTACATTT 8 29 0 TTTATTAATT 0.865508 -215 TTTTTTTACCCAAGCATTTATTTCAACTTTTTT 8 62 0 CAGATTATTT 0.712369 -182 TCTTTAGAAGCTTTTCTTCATTTACCAGAACTT 8 153 0 CTTCTTATTT 0.918299 -91 TTTTGATCAACAGTCCTTGAATTTTAATGCAAT 8 210 0 CATCTTAATT 0.9469 -34 TCCTTCCGGGCTTTACATAAATTAATTGAATTA 9 20 1 CTTCATAATT 0.925588 -71 GTTTTTTGTGCTATAATTCAATTAATTTATGTA 9 33 0 CTTATTAATT 0.988852 -58 TCTTTAAATTCATTCAATAAATTCAATAATATT 11 13 0 CATAATAATT 0.818914 -104 CATAAATATACTTGGATTTAATTTATAATTAAT 11 66 0 CTGATTAATT 0.968838 -51 AATAACTTTCCTTTGATTAAATTAAATCCATAA 11 94 0 CTTATTAATT 0.988407 -23 ** * *** **** Masking position 10 Map Score: 12.7673 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 214 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 ATAAAAATTGTTAAATGTTTTTTTTAAAAAAAGT 1 81 1 TAATTTTTTT 0.978967 -76 TTATTATAGCTTAAAACTTTTTTTAAAAAAAACA 1 96 0 TAATTTTTTT 0.97891 -61 TTATTTAAAATTGCATTTTTATTTTTAATCTTTC 4 17 0 TCATTTATTT 0.842329 -137 TATGATTTAATGTAAATTTTAATTACCGCCTAAA 4 96 1 TAATTTAATT 0.79688 -58 TTTATACCATTTAAAGCCTTTTTTAGGCGGTAAT 4 117 0 TAACTTTTTT 0.963054 -37 CTTAGAGAAGTAAAAATCTTTTTTCTATTAATTT 6 16 0 TAACTTTTTT 0.947897 -32 AACGAGCTGATTTAACAATTATTTATTCTTTTTT 7 30 1 TAAATTATTT 0.82657 -39 AAGCATTTATTTCAACTTTTTTGTCTATCAATTT 8 50 0 TAATTTTTGT 0.880304 -194 TTCCGTGGTGTCTAATTTTTTTTACCCAAGCATT 8 77 0 TAATTTTTTA 0.832028 -167 CTGCGATCTTTAGAAGCTTTTCTTCATTTACCAG 8 158 0 TAATTTTCTT 0.888934 -86 TAATGCAATATTCAAGTTTTATTTTTTCTGCGAT 8 185 0 TAATTTATTT 0.971323 -59 GGGTTTTTATTGGAAGGCTTGTTTGTTTTTTGTG 9 56 0 TAACTTGTTT 0.873797 -35 TTGAATGAATTTAAAGATTAATTTAGTATATTAT 11 29 1 TAATTAATTT 0.782822 -88 * ** ******* Masking position 5 Map Score: 13.8977 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 553 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 ATAATAATCACCCCTAAAAAGTAAAGTATAA 1 17 1 CCCTAAAAAG 0.985113 -140 GGTATTAATTCTCCTAAATAATTGACTTAAA 2 15 1 CCCTAAATAA 0.978095 -47 TTTTAATTACCGCCTAAAAAAGGCTTTAAAT 4 112 1 CCCTAAAAAA 0.993239 -42 ATAACAATTCCTCCTAAAAAAGAATAAATAA 7 48 0 CCCTAAAAAA 0.993238 -21 TTCTAAAGATCGCAGAAAAAATAAAACTTGA 8 177 1 CCAGAAAAAA 0.926911 -67 * ********* Masking position 6 Map Score: 5.09592 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AAGATATTTCCTTTTGTTTTTAT 5 11 0 ATATTTCCTT 0.925444 -13 TAGAAAAAAGATTTTTACTTCTCTAAGAGA 6 23 1 ATTTTTACTT 0.802683 -25 TTGTCTATCAATTTTTCATTCAATTCATTA 8 34 0 ATTTTTCATT 0.802686 -210 TAGAAAGATAAATTTTCCGTGGTGTCTAAT 8 95 0 AATTTTCCGT 0.926286 -149 TCTTTTGATCAACAGTCCTTGAATTTTAAT 8 215 0 AACAGTCCTT 0.804003 -29 ATTAAACTTTCCTTCCGGGCTTTA 9 5 1 AACTTTCCTT 0.984665 -86 AATAACTTTCCTTTGATTAAATT 11 104 0 AACTTTCCTT 0.984665 -13 ********** Masking position 1 Map Score: 2.61083 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 136 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: -1.07759e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: -1.07759e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: -1.07759e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0